Starting phenix.real_space_refine on Fri Jun 20 01:19:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzl_36746/06_2025/8jzl_36746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzl_36746/06_2025/8jzl_36746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzl_36746/06_2025/8jzl_36746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzl_36746/06_2025/8jzl_36746.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzl_36746/06_2025/8jzl_36746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzl_36746/06_2025/8jzl_36746.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 14538 2.51 5 N 4212 2.21 5 O 4344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23184 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 11.18, per 1000 atoms: 0.48 Number of scatterers: 23184 At special positions: 0 Unit cell: (156.782, 144.896, 125.086, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 4344 8.00 N 4212 7.00 C 14538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 3.1 seconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 56.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.848A pdb=" N GLN A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.596A pdb=" N ASN A 536 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 143 removed outlier: 4.648A pdb=" N LYS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.848A pdb=" N GLN B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 520 Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN B 536 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 280 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.726A pdb=" N MET C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN C 536 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 4.130A pdb=" N ARG C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE C 559 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 92 removed outlier: 3.587A pdb=" N LEU D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 280 Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'D' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 406 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG D 444 " --> pdb=" O LYS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 483 removed outlier: 3.850A pdb=" N GLN D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU D 507 " --> pdb=" O GLN D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 520 Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN D 536 " --> pdb=" O GLU D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.130A pdb=" N ARG D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE D 559 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 92 removed outlier: 3.589A pdb=" N LEU E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 280 Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET E 316 " --> pdb=" O LYS E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 406 Processing helix chain 'E' and resid 411 through 429 Processing helix chain 'E' and resid 430 through 433 Processing helix chain 'E' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG E 444 " --> pdb=" O LYS E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU E 507 " --> pdb=" O GLN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 520 Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN E 536 " --> pdb=" O GLU E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG E 542 " --> pdb=" O SER E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 555 through 559 removed outlier: 3.753A pdb=" N ILE E 559 " --> pdb=" O SER E 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 92 removed outlier: 3.589A pdb=" N LEU F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 280 Processing helix chain 'F' and resid 281 through 290 Processing helix chain 'F' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET F 316 " --> pdb=" O LYS F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU F 381 " --> pdb=" O SER F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 411 through 429 Processing helix chain 'F' and resid 430 through 433 Processing helix chain 'F' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG F 444 " --> pdb=" O LYS F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU F 507 " --> pdb=" O GLN F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 520 Processing helix chain 'F' and resid 532 through 536 removed outlier: 3.594A pdb=" N ASN F 536 " --> pdb=" O GLU F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG F 542 " --> pdb=" O SER F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 555 through 559 removed outlier: 3.753A pdb=" N ILE F 559 " --> pdb=" O SER F 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS A 184 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 233 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A 241 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU A 235 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 294 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP A 353 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 296 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA A 355 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 298 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A 357 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 300 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE A 197 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS B 184 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 233 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR B 241 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 235 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 294 " --> pdb=" O LYS B 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP B 353 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 296 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA B 355 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 298 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE B 357 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 300 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE B 197 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS C 184 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 233 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR C 241 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU C 235 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 294 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP C 353 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 296 " --> pdb=" O ASP C 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA C 355 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 298 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 357 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 300 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE C 197 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 200 " --> pdb=" O ILE C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS D 184 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 233 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR D 241 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU D 235 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 294 " --> pdb=" O LYS D 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP D 353 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 296 " --> pdb=" O ASP D 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA D 355 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 298 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE D 357 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER D 300 " --> pdb=" O PHE D 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE D 197 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS D 200 " --> pdb=" O ILE D 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS E 184 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 233 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR E 241 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU E 235 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL E 294 " --> pdb=" O LYS E 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP E 353 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 296 " --> pdb=" O ASP E 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA E 355 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 298 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE E 357 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 300 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE E 197 " --> pdb=" O LYS E 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS E 200 " --> pdb=" O ILE E 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS F 184 " --> pdb=" O HIS F 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 233 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR F 241 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU F 235 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 294 " --> pdb=" O LYS F 351 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP F 353 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 296 " --> pdb=" O ASP F 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA F 355 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 298 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 357 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER F 300 " --> pdb=" O PHE F 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE F 197 " --> pdb=" O LYS F 200 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS F 200 " --> pdb=" O ILE F 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1320 hydrogen bonds defined for protein. 3816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7772 1.33 - 1.45: 2449 1.45 - 1.57: 13245 1.57 - 1.68: 0 1.68 - 1.80: 162 Bond restraints: 23628 Sorted by residual: bond pdb=" C LEU E 251 " pdb=" N SER E 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.75e+00 bond pdb=" C LEU D 251 " pdb=" N SER D 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.73e+00 bond pdb=" C LEU A 251 " pdb=" N SER A 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.73e+00 bond pdb=" C LEU F 251 " pdb=" N SER F 252 " ideal model delta sigma weight residual 1.333 1.298 0.034 1.59e-02 3.96e+03 4.70e+00 bond pdb=" C LEU C 251 " pdb=" N SER C 252 " ideal model delta sigma weight residual 1.333 1.298 0.034 1.59e-02 3.96e+03 4.70e+00 ... (remaining 23623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 30939 1.65 - 3.30: 863 3.30 - 4.95: 100 4.95 - 6.60: 36 6.60 - 8.25: 6 Bond angle restraints: 31944 Sorted by residual: angle pdb=" C LEU F 76 " pdb=" N TYR F 77 " pdb=" CA TYR F 77 " ideal model delta sigma weight residual 120.82 125.22 -4.40 1.50e+00 4.44e-01 8.59e+00 angle pdb=" C LEU C 76 " pdb=" N TYR C 77 " pdb=" CA TYR C 77 " ideal model delta sigma weight residual 120.82 125.21 -4.39 1.50e+00 4.44e-01 8.56e+00 angle pdb=" C LEU D 76 " pdb=" N TYR D 77 " pdb=" CA TYR D 77 " ideal model delta sigma weight residual 120.82 125.20 -4.38 1.50e+00 4.44e-01 8.51e+00 angle pdb=" C LEU E 76 " pdb=" N TYR E 77 " pdb=" CA TYR E 77 " ideal model delta sigma weight residual 120.82 125.14 -4.32 1.50e+00 4.44e-01 8.31e+00 angle pdb=" C LEU B 76 " pdb=" N TYR B 77 " pdb=" CA TYR B 77 " ideal model delta sigma weight residual 120.82 125.14 -4.32 1.50e+00 4.44e-01 8.29e+00 ... (remaining 31939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 13174 17.48 - 34.96: 980 34.96 - 52.44: 168 52.44 - 69.92: 42 69.92 - 87.40: 12 Dihedral angle restraints: 14376 sinusoidal: 5796 harmonic: 8580 Sorted by residual: dihedral pdb=" CA TYR D 254 " pdb=" C TYR D 254 " pdb=" N HIS D 255 " pdb=" CA HIS D 255 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA TYR B 254 " pdb=" C TYR B 254 " pdb=" N HIS B 255 " pdb=" CA HIS B 255 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR A 254 " pdb=" C TYR A 254 " pdb=" N HIS A 255 " pdb=" CA HIS A 255 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 14373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1871 0.031 - 0.062: 1120 0.062 - 0.093: 368 0.093 - 0.124: 134 0.124 - 0.154: 53 Chirality restraints: 3546 Sorted by residual: chirality pdb=" CA GLU A 318 " pdb=" N GLU A 318 " pdb=" C GLU A 318 " pdb=" CB GLU A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA GLU D 318 " pdb=" N GLU D 318 " pdb=" C GLU D 318 " pdb=" CB GLU D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA GLU F 318 " pdb=" N GLU F 318 " pdb=" C GLU F 318 " pdb=" CB GLU F 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 3543 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 351 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO E 352 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 352 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 352 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 351 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO F 352 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO F 352 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 352 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 351 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 352 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " -0.019 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8046 2.86 - 3.37: 22625 3.37 - 3.88: 37210 3.88 - 4.39: 42374 4.39 - 4.90: 72167 Nonbonded interactions: 182422 Sorted by model distance: nonbonded pdb=" O LYS A 464 " pdb=" NE2 GLN A 515 " model vdw 2.353 3.120 nonbonded pdb=" O LYS F 464 " pdb=" NE2 GLN F 515 " model vdw 2.353 3.120 nonbonded pdb=" O LYS C 464 " pdb=" NE2 GLN C 515 " model vdw 2.354 3.120 nonbonded pdb=" O LYS E 464 " pdb=" NE2 GLN E 515 " model vdw 2.354 3.120 nonbonded pdb=" O LYS D 464 " pdb=" NE2 GLN D 515 " model vdw 2.354 3.120 ... (remaining 182417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.220 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 48.800 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.040 23628 Z= 0.373 Angle : 0.670 8.247 31944 Z= 0.357 Chirality : 0.045 0.154 3546 Planarity : 0.003 0.034 4164 Dihedral : 12.906 87.398 8832 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2976 helix: 1.93 (0.13), residues: 1542 sheet: 1.15 (0.26), residues: 396 loop : -1.09 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 227 HIS 0.006 0.001 HIS F 482 PHE 0.017 0.002 PHE C 502 TYR 0.015 0.002 TYR D 77 ARG 0.003 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.15965 ( 1320) hydrogen bonds : angle 6.10736 ( 3816) covalent geometry : bond 0.00854 (23628) covalent geometry : angle 0.67041 (31944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9232 (m110) cc_final: 0.8920 (m-40) REVERT: A 105 MET cc_start: 0.9170 (tpt) cc_final: 0.8908 (tmt) REVERT: A 547 ASN cc_start: 0.9250 (m-40) cc_final: 0.8981 (m110) REVERT: B 546 GLU cc_start: 0.8600 (tp30) cc_final: 0.8399 (tp30) REVERT: C 465 ASP cc_start: 0.8410 (m-30) cc_final: 0.8159 (m-30) REVERT: D 105 MET cc_start: 0.9272 (tpt) cc_final: 0.8421 (tmm) REVERT: D 220 ILE cc_start: 0.9376 (pt) cc_final: 0.9161 (pp) REVERT: E 105 MET cc_start: 0.9148 (tpt) cc_final: 0.8245 (tmm) REVERT: E 547 ASN cc_start: 0.9360 (m-40) cc_final: 0.9115 (m-40) REVERT: F 543 VAL cc_start: 0.8805 (t) cc_final: 0.8506 (p) outliers start: 0 outliers final: 1 residues processed: 235 average time/residue: 1.3050 time to fit residues: 354.1314 Evaluate side-chains 173 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 432 HIS A 540 GLN B 103 ASN B 325 GLN B 432 HIS C 103 ASN C 432 HIS D 103 ASN D 432 HIS E 103 ASN E 432 HIS E 515 GLN F 103 ASN F 432 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.113001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.068366 restraints weight = 47149.367| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.34 r_work: 0.2603 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23628 Z= 0.119 Angle : 0.564 7.006 31944 Z= 0.292 Chirality : 0.040 0.163 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.206 14.254 3140 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.69 % Allowed : 6.84 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.16), residues: 2976 helix: 2.57 (0.13), residues: 1518 sheet: 1.19 (0.25), residues: 420 loop : -1.11 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 549 HIS 0.003 0.001 HIS D 485 PHE 0.011 0.001 PHE E 357 TYR 0.019 0.001 TYR D 77 ARG 0.006 0.000 ARG B 159 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1320) hydrogen bonds : angle 4.42052 ( 3816) covalent geometry : bond 0.00249 (23628) covalent geometry : angle 0.56448 (31944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8883 (mp10) REVERT: A 81 ARG cc_start: 0.8853 (ptp-110) cc_final: 0.8133 (ptp-110) REVERT: A 105 MET cc_start: 0.9286 (tpt) cc_final: 0.8854 (tmt) REVERT: A 547 ASN cc_start: 0.9313 (m-40) cc_final: 0.9053 (m110) REVERT: B 546 GLU cc_start: 0.8209 (tp30) cc_final: 0.7991 (tp30) REVERT: D 105 MET cc_start: 0.9056 (tpt) cc_final: 0.8165 (tmm) REVERT: D 220 ILE cc_start: 0.9306 (pt) cc_final: 0.9086 (pp) REVERT: D 551 SER cc_start: 0.9348 (t) cc_final: 0.8927 (p) REVERT: E 80 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8902 (mp10) REVERT: F 471 ASP cc_start: 0.8969 (t0) cc_final: 0.8740 (t0) outliers start: 17 outliers final: 2 residues processed: 223 average time/residue: 1.2927 time to fit residues: 332.5875 Evaluate side-chains 196 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 4 optimal weight: 30.0000 chunk 245 optimal weight: 50.0000 chunk 78 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 222 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.067925 restraints weight = 47247.331| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.34 r_work: 0.2559 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23628 Z= 0.133 Angle : 0.534 7.521 31944 Z= 0.272 Chirality : 0.039 0.181 3546 Planarity : 0.003 0.050 4164 Dihedral : 3.979 13.812 3140 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.40 % Allowed : 9.71 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 2976 helix: 2.60 (0.13), residues: 1560 sheet: 1.19 (0.26), residues: 402 loop : -0.94 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 549 HIS 0.005 0.001 HIS A 485 PHE 0.008 0.001 PHE E 357 TYR 0.017 0.001 TYR A 77 ARG 0.006 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1320) hydrogen bonds : angle 4.12916 ( 3816) covalent geometry : bond 0.00298 (23628) covalent geometry : angle 0.53387 (31944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9250 (tpt) cc_final: 0.8648 (tmm) REVERT: A 267 GLU cc_start: 0.8760 (tp30) cc_final: 0.8339 (mm-30) REVERT: A 547 ASN cc_start: 0.9295 (m-40) cc_final: 0.9041 (m110) REVERT: D 105 MET cc_start: 0.9025 (tpt) cc_final: 0.8124 (tmm) REVERT: D 220 ILE cc_start: 0.9412 (pt) cc_final: 0.9184 (pp) REVERT: D 318 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: D 551 SER cc_start: 0.9341 (t) cc_final: 0.8921 (p) REVERT: E 105 MET cc_start: 0.8918 (tpt) cc_final: 0.8715 (tpt) REVERT: F 318 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8455 (mp0) outliers start: 10 outliers final: 4 residues processed: 213 average time/residue: 1.4392 time to fit residues: 350.6184 Evaluate side-chains 191 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 526 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 157 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 222 optimal weight: 0.0770 chunk 160 optimal weight: 7.9990 chunk 122 optimal weight: 0.0470 chunk 103 optimal weight: 0.8980 chunk 124 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 135 optimal weight: 3.9990 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.070393 restraints weight = 47370.208| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.36 r_work: 0.2651 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23628 Z= 0.086 Angle : 0.507 8.015 31944 Z= 0.254 Chirality : 0.038 0.162 3546 Planarity : 0.003 0.055 4164 Dihedral : 3.733 13.399 3138 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.69 % Allowed : 11.00 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.16), residues: 2976 helix: 2.89 (0.13), residues: 1524 sheet: 1.18 (0.26), residues: 420 loop : -0.96 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.002 0.000 HIS F 255 PHE 0.006 0.001 PHE D 357 TYR 0.018 0.001 TYR A 77 ARG 0.006 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.02891 ( 1320) hydrogen bonds : angle 3.96422 ( 3816) covalent geometry : bond 0.00181 (23628) covalent geometry : angle 0.50658 (31944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9265 (tpt) cc_final: 0.8691 (tmm) REVERT: A 267 GLU cc_start: 0.8722 (tp30) cc_final: 0.8269 (mm-30) REVERT: A 547 ASN cc_start: 0.9330 (m-40) cc_final: 0.9107 (m110) REVERT: C 318 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: D 105 MET cc_start: 0.9077 (tpt) cc_final: 0.8185 (tmm) REVERT: D 220 ILE cc_start: 0.9377 (pt) cc_final: 0.9155 (pp) REVERT: D 471 ASP cc_start: 0.8968 (t0) cc_final: 0.8760 (t0) REVERT: D 551 SER cc_start: 0.9321 (t) cc_final: 0.8913 (p) REVERT: E 80 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8937 (mp10) REVERT: F 318 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8465 (mp0) outliers start: 17 outliers final: 2 residues processed: 217 average time/residue: 1.4482 time to fit residues: 359.4219 Evaluate side-chains 196 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain E residue 80 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 163 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.0050 chunk 285 optimal weight: 0.9990 chunk 251 optimal weight: 30.0000 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 289 optimal weight: 0.7980 chunk 246 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.069936 restraints weight = 47323.651| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.36 r_work: 0.2645 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23628 Z= 0.091 Angle : 0.521 9.114 31944 Z= 0.259 Chirality : 0.038 0.169 3546 Planarity : 0.003 0.044 4164 Dihedral : 3.641 14.328 3138 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.73 % Allowed : 11.81 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2976 helix: 2.77 (0.13), residues: 1566 sheet: 1.06 (0.25), residues: 432 loop : -0.79 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 549 HIS 0.003 0.000 HIS F 485 PHE 0.006 0.001 PHE E 357 TYR 0.014 0.001 TYR A 77 ARG 0.007 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 1320) hydrogen bonds : angle 3.87926 ( 3816) covalent geometry : bond 0.00203 (23628) covalent geometry : angle 0.52103 (31944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8869 (mp10) REVERT: A 105 MET cc_start: 0.9281 (tpt) cc_final: 0.8715 (tmm) REVERT: A 267 GLU cc_start: 0.8704 (tp30) cc_final: 0.8230 (mm-30) REVERT: A 547 ASN cc_start: 0.9330 (m-40) cc_final: 0.9112 (m110) REVERT: C 318 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: D 220 ILE cc_start: 0.9389 (pt) cc_final: 0.9174 (pp) REVERT: D 318 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: D 547 ASN cc_start: 0.9152 (m110) cc_final: 0.8938 (m-40) REVERT: D 551 SER cc_start: 0.9310 (t) cc_final: 0.8905 (p) REVERT: E 80 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: E 85 THR cc_start: 0.9341 (m) cc_final: 0.9134 (p) REVERT: F 80 GLN cc_start: 0.8890 (mp10) cc_final: 0.8616 (mp10) REVERT: F 318 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8492 (mp0) outliers start: 18 outliers final: 5 residues processed: 222 average time/residue: 1.5774 time to fit residues: 401.6728 Evaluate side-chains 207 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 71 optimal weight: 0.8980 chunk 267 optimal weight: 0.0010 chunk 182 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 147 optimal weight: 50.0000 chunk 97 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.068654 restraints weight = 47621.634| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.32 r_work: 0.2574 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23628 Z= 0.116 Angle : 0.542 10.005 31944 Z= 0.269 Chirality : 0.038 0.180 3546 Planarity : 0.003 0.036 4164 Dihedral : 3.725 14.812 3138 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.85 % Allowed : 12.14 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2976 helix: 3.06 (0.13), residues: 1518 sheet: 1.05 (0.25), residues: 432 loop : -0.87 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 549 HIS 0.004 0.001 HIS E 482 PHE 0.007 0.001 PHE F 203 TYR 0.012 0.001 TYR C 77 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 1320) hydrogen bonds : angle 3.89401 ( 3816) covalent geometry : bond 0.00268 (23628) covalent geometry : angle 0.54212 (31944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 6.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8873 (mp10) REVERT: A 105 MET cc_start: 0.9294 (tpt) cc_final: 0.8684 (tmm) REVERT: A 267 GLU cc_start: 0.8721 (tp30) cc_final: 0.8385 (mm-30) REVERT: A 318 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8580 (mp0) REVERT: A 547 ASN cc_start: 0.9319 (m-40) cc_final: 0.9101 (m110) REVERT: B 318 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8620 (mp0) REVERT: C 318 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: C 368 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8261 (pp) REVERT: D 220 ILE cc_start: 0.9385 (pt) cc_final: 0.9180 (pp) REVERT: D 551 SER cc_start: 0.9294 (t) cc_final: 0.8882 (p) REVERT: E 80 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: E 85 THR cc_start: 0.9300 (m) cc_final: 0.9086 (p) REVERT: F 80 GLN cc_start: 0.8934 (mp10) cc_final: 0.8616 (mp10) REVERT: F 105 MET cc_start: 0.8800 (tpt) cc_final: 0.8333 (ppp) REVERT: F 318 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8511 (mp0) REVERT: F 368 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (pp) outliers start: 21 outliers final: 5 residues processed: 211 average time/residue: 1.9867 time to fit residues: 496.0957 Evaluate side-chains 200 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.064625 restraints weight = 47577.481| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.33 r_work: 0.2542 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23628 Z= 0.265 Angle : 0.638 9.251 31944 Z= 0.324 Chirality : 0.042 0.196 3546 Planarity : 0.003 0.042 4164 Dihedral : 4.303 18.213 3138 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.01 % Allowed : 12.54 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.16), residues: 2976 helix: 2.83 (0.13), residues: 1554 sheet: 1.11 (0.26), residues: 402 loop : -0.84 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 549 HIS 0.007 0.001 HIS A 485 PHE 0.016 0.002 PHE F 203 TYR 0.013 0.002 TYR C 77 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 1320) hydrogen bonds : angle 4.12779 ( 3816) covalent geometry : bond 0.00626 (23628) covalent geometry : angle 0.63790 (31944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8855 (mp10) REVERT: A 105 MET cc_start: 0.9290 (tpt) cc_final: 0.8652 (tmm) REVERT: A 267 GLU cc_start: 0.8782 (tp30) cc_final: 0.8283 (mm-30) REVERT: A 318 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8699 (mp0) REVERT: A 547 ASN cc_start: 0.9304 (m-40) cc_final: 0.9087 (m110) REVERT: B 316 MET cc_start: 0.8717 (mtm) cc_final: 0.8473 (mtm) REVERT: B 318 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8628 (mp0) REVERT: C 368 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8553 (pp) REVERT: D 105 MET cc_start: 0.9115 (tpt) cc_final: 0.8892 (tpt) REVERT: E 80 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: E 85 THR cc_start: 0.9312 (m) cc_final: 0.9085 (p) REVERT: E 318 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8604 (mp0) REVERT: F 80 GLN cc_start: 0.8988 (mp10) cc_final: 0.8594 (mp10) REVERT: F 105 MET cc_start: 0.8820 (tpt) cc_final: 0.8359 (ppp) REVERT: F 318 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8579 (mp0) REVERT: F 368 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8536 (pp) outliers start: 25 outliers final: 6 residues processed: 217 average time/residue: 1.3517 time to fit residues: 336.8895 Evaluate side-chains 201 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 485 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 249 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065421 restraints weight = 47638.119| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.28 r_work: 0.2492 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23628 Z= 0.210 Angle : 0.611 9.628 31944 Z= 0.307 Chirality : 0.041 0.198 3546 Planarity : 0.003 0.041 4164 Dihedral : 4.205 17.150 3138 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.77 % Allowed : 13.03 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2976 helix: 3.00 (0.13), residues: 1512 sheet: 1.06 (0.25), residues: 420 loop : -0.97 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 549 HIS 0.006 0.001 HIS A 485 PHE 0.013 0.001 PHE F 203 TYR 0.015 0.002 TYR D 254 ARG 0.006 0.000 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 1320) hydrogen bonds : angle 4.06320 ( 3816) covalent geometry : bond 0.00495 (23628) covalent geometry : angle 0.61074 (31944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8857 (mp10) REVERT: A 105 MET cc_start: 0.9290 (tpt) cc_final: 0.8643 (tmm) REVERT: A 159 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7479 (tmt170) REVERT: A 267 GLU cc_start: 0.8737 (tp30) cc_final: 0.8229 (mm-30) REVERT: A 318 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8648 (mp0) REVERT: A 547 ASN cc_start: 0.9290 (m-40) cc_final: 0.9078 (m110) REVERT: B 316 MET cc_start: 0.8653 (mtm) cc_final: 0.8393 (mtm) REVERT: B 318 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8693 (mp0) REVERT: C 368 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8463 (pp) REVERT: D 105 MET cc_start: 0.9118 (tpt) cc_final: 0.8894 (tpt) REVERT: D 318 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: E 80 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8671 (mp10) REVERT: E 316 MET cc_start: 0.8682 (mtm) cc_final: 0.8413 (mtm) REVERT: E 318 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8686 (mp0) REVERT: F 80 GLN cc_start: 0.8988 (mp10) cc_final: 0.8614 (mp10) REVERT: F 105 MET cc_start: 0.8841 (tpt) cc_final: 0.8351 (ppp) REVERT: F 318 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8505 (mp0) REVERT: F 368 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8452 (pp) outliers start: 19 outliers final: 7 residues processed: 210 average time/residue: 1.3681 time to fit residues: 330.6135 Evaluate side-chains 204 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 267 optimal weight: 0.9990 chunk 282 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 62 optimal weight: 0.0070 chunk 120 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.071885 restraints weight = 47907.345| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.34 r_work: 0.2757 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23628 Z= 0.094 Angle : 0.554 9.817 31944 Z= 0.274 Chirality : 0.038 0.206 3546 Planarity : 0.003 0.035 4164 Dihedral : 3.748 15.501 3138 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.53 % Allowed : 13.55 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.16), residues: 2976 helix: 2.86 (0.13), residues: 1560 sheet: 0.99 (0.25), residues: 432 loop : -0.79 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 549 HIS 0.003 0.000 HIS A 485 PHE 0.006 0.001 PHE D 357 TYR 0.011 0.001 TYR C 77 ARG 0.005 0.000 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 1320) hydrogen bonds : angle 3.89436 ( 3816) covalent geometry : bond 0.00209 (23628) covalent geometry : angle 0.55439 (31944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8860 (mp10) REVERT: A 105 MET cc_start: 0.9274 (tpt) cc_final: 0.8628 (tmm) REVERT: A 159 ARG cc_start: 0.7801 (ttt-90) cc_final: 0.7515 (tmt170) REVERT: A 267 GLU cc_start: 0.8705 (tp30) cc_final: 0.8321 (mm-30) REVERT: A 547 ASN cc_start: 0.9309 (m-40) cc_final: 0.9099 (m110) REVERT: B 316 MET cc_start: 0.8610 (mtm) cc_final: 0.8321 (mtm) REVERT: B 318 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8650 (mp0) REVERT: C 318 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: D 105 MET cc_start: 0.9117 (tpt) cc_final: 0.8900 (tpt) REVERT: D 318 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: E 80 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8671 (mp10) REVERT: E 316 MET cc_start: 0.8674 (mtm) cc_final: 0.8338 (mtm) REVERT: E 318 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8641 (mp0) REVERT: F 105 MET cc_start: 0.8860 (tpt) cc_final: 0.8368 (ppp) REVERT: F 316 MET cc_start: 0.8614 (mtm) cc_final: 0.8348 (mtm) REVERT: F 318 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8477 (mp0) outliers start: 13 outliers final: 4 residues processed: 211 average time/residue: 1.3986 time to fit residues: 343.9619 Evaluate side-chains 198 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 143 optimal weight: 7.9990 chunk 131 optimal weight: 0.0470 chunk 129 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 132 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.114470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.070931 restraints weight = 47875.087| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.35 r_work: 0.2745 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23628 Z= 0.106 Angle : 0.563 10.028 31944 Z= 0.280 Chirality : 0.039 0.219 3546 Planarity : 0.003 0.029 4164 Dihedral : 3.737 15.684 3138 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.49 % Allowed : 13.96 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.16), residues: 2976 helix: 2.89 (0.13), residues: 1560 sheet: 1.00 (0.25), residues: 432 loop : -0.76 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 549 HIS 0.004 0.001 HIS A 485 PHE 0.006 0.001 PHE D 357 TYR 0.011 0.001 TYR C 77 ARG 0.005 0.000 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 1320) hydrogen bonds : angle 3.90093 ( 3816) covalent geometry : bond 0.00245 (23628) covalent geometry : angle 0.56295 (31944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9223 (mp10) cc_final: 0.8848 (mp10) REVERT: A 105 MET cc_start: 0.9273 (tpt) cc_final: 0.8625 (tmm) REVERT: A 159 ARG cc_start: 0.7803 (ttt-90) cc_final: 0.7498 (tmt170) REVERT: A 267 GLU cc_start: 0.8703 (tp30) cc_final: 0.8298 (mm-30) REVERT: B 316 MET cc_start: 0.8614 (mtm) cc_final: 0.8327 (mtm) REVERT: B 318 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8657 (mp0) REVERT: C 318 GLU cc_start: 0.8460 (mp0) cc_final: 0.8207 (mp0) REVERT: D 105 MET cc_start: 0.9130 (tpt) cc_final: 0.8910 (tpt) REVERT: D 318 GLU cc_start: 0.8402 (mp0) cc_final: 0.8064 (mp0) REVERT: E 80 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: E 85 THR cc_start: 0.9323 (m) cc_final: 0.9099 (p) REVERT: E 316 MET cc_start: 0.8708 (mtm) cc_final: 0.8379 (mtm) REVERT: E 318 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8654 (mp0) REVERT: F 80 GLN cc_start: 0.8978 (mp10) cc_final: 0.8550 (mp10) REVERT: F 105 MET cc_start: 0.8855 (tpt) cc_final: 0.8362 (ppp) REVERT: F 316 MET cc_start: 0.8689 (mtm) cc_final: 0.8458 (mtm) REVERT: F 318 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8528 (mp0) outliers start: 12 outliers final: 7 residues processed: 200 average time/residue: 1.3285 time to fit residues: 305.9845 Evaluate side-chains 198 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 19 optimal weight: 0.8980 chunk 122 optimal weight: 0.0370 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 overall best weight: 2.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.069185 restraints weight = 47884.903| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.33 r_work: 0.2686 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23628 Z= 0.168 Angle : 0.597 10.509 31944 Z= 0.297 Chirality : 0.040 0.219 3546 Planarity : 0.003 0.028 4164 Dihedral : 3.902 17.113 3138 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.49 % Allowed : 14.24 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.16), residues: 2976 helix: 2.92 (0.13), residues: 1554 sheet: 0.96 (0.25), residues: 432 loop : -0.76 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 549 HIS 0.005 0.001 HIS A 485 PHE 0.011 0.001 PHE F 203 TYR 0.018 0.001 TYR D 254 ARG 0.008 0.000 ARG E 159 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1320) hydrogen bonds : angle 3.95998 ( 3816) covalent geometry : bond 0.00394 (23628) covalent geometry : angle 0.59737 (31944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20055.71 seconds wall clock time: 349 minutes 38.49 seconds (20978.49 seconds total)